Abstract SP112: Spatial variance signatures/Intra-tumor zonation in TNBC

It is increasingly clear that triple negative breast cancer (TNBC) is a heterogeneous disease with variable clinical presentation, histological features and response to therapy. While these differences have been partially explained by inter- and intra-tumoral heterogeneity, spatial heterogeneity represented by the tumor architecture plays a critical role in clonal evolution and displays a landscape for different compartment-specific processes and cell-to-cell specific interactions. To better understand the impact of spatial heterogeneity on gene-expression-defined cell populations, we have coupled single-cell RNA sequencing with multiplex immunofluorescence (IF). Multiplex immunofluorescence using specific markers for each cell cluster, integrated with computational image analyses and neighborhood maps, has revealed spatial zonation of single cell subpopulations. Zonation of single cell populations was coupled to hypoxia and overlayed distinct metabolic tumor zones and defined areas of differential stress and cell plasticity that give rise to tumor cells with enhanced fitness and aggressivity.

Citation Format: M Park, C Martínez Ramirez, Y Yang, A Blanchet-Cohen, H Kuasne, A Fortier, J Ragoussis, P Savage, A Omeroglou, S Meterissian, S Costantino, C Kleinman. Spatial variance signatures/Intra-tumor zonation in TNBC [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP112.

Abstract B14: Pinpointing the origins of pediatric brain tumors using single-cell transcriptomic analysis

Childhood tumors of the central nervous system are deadly diseases, and for many tumor types outcome has not improved over the last three decades. Current evidence supports a model in which genetic alterations drive changes in neurodevelopmental gene expression programs, leading to oncogenesis postnatally. We hypothesize that there are specific cellular states during normal brain development that are vulnerable targets for oncogenic mutations. However, comprehensive developmental data for many brain regions relevant to pediatric brain tumors (PBT) are lacking. Here, we leverage single-cell RNA-sequencing to generate a reference transcriptome atlas of the developing brain in two regions where PBT commonly arise, the forebrain and the pons. We profile >65,000 cells from healthy embryonic and neonatal mouse and human specimens, and characterize cellular diversity, dynamics related to differentiation, and transcription factor regulatory activity. We use a novel strategy to project bulk RNA-seq profiles for a cohort of 200 PBT onto these cell types. We show that this projection stratifies tumors by type, and for several PBT subtypes, we identify their closest transcriptional match among the cell populations of the normal developing brain. WNT-subtype medulloblastoma matches the lower rhombic-lip derived mossy fiber neuron lineage. In embryonal tumors with multilayered rosettes, we identify prenatal neurogenic radial glial cells as candidate cells of origin, while Group 2a/b atypical teratoid/rhabdoid tumors originate outside the neuro-ectoderm. Finally, single-cell profiling of patient tumor samples shows that these tumors mimic the transcriptional programs of their corresponding normal lineages and contain a mixture of cells with varying degrees of differentiation. We identify impaired differentiation of specific neural progenitors as a common oncogenic mechanism underlying PBT, and further demonstrate that this differentiation blockade may be reversible. Our findings thus provide a rational framework to guide future modeling and therapeutics. More broadly, we assemble a high-resolution developmental dataset, a valuable resource for the study of neuroscience and many brain pathologies.

Citation Format: Selin Jessa, Alexis Blanchet-Cohen, Brian Krug, Maria C. Vladoiu, Marie Coutelier, Damien Faury, Brice Poreau, Nicolas De Jay, W. Todd Farmer, Yixing Hu, Steven Hébert, Jean Monlong, Keith K. Murai, Melissa McConechy, Guillaume Bourque, Jiannis Ragoussis, Livia Garzia, Michael D. Taylor, Nada Jabado, Claudia L. Kleinman. Pinpointing the origins of pediatric brain tumors using single-cell transcriptomic analysis [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B14.

Stalled developmental programs at the root of pediatric brain tumors

Childhood brain tumors have suspected prenatal origins. To identify vulnerable developmental states, we generated a single-cell transcriptome atlas of >65,000 cells from embryonal pons and forebrain, two major tumor locations. We derived signatures for 191 distinct cell populations and defined regional cellular diversity and differentiation dynamics. Projection of bulk tumor transcriptomes onto this dataset shows that WNT medulloblastomas match the rhombic lip-derived mossy fiber neuronal lineage, embryonal tumors with multilayered rosettes fully recapitulate a neuronal lineage, while Group 2a/b atypical teratoid/rhabdoid tumors may originate outside of the neuroectoderm. Importantly, single-cell tumor profiles reveal highly defined cell hierarchies mirroring transcriptional programs of the corresponding normal lineages. Our findings identify impaired differentiation of specific neural progenitors as a common mechanism underlying these pediatric cancers and provide a rational framework for future modeling and therapeutic interventions.

Loss of human ICOSL results in combined immunodeficiency

Primary immunodeficiencies represent naturally occurring experimental models to decipher human immunobiology. We report a patient with combined immunodeficiency, marked by recurrent respiratory tract and DNA-based viral infections, hypogammaglobulinemia, and panlymphopenia. He also developed moderate neutropenia but without prototypical pyogenic infections. Using whole-exome sequencing, we identified a homozygous mutation in the inducible T cell costimulator ligand gene (ICOSLG; c.657C>G; p.N219K). Whereas WT ICOSL is expressed at the cell surface, the ICOSL^N219K mutation abrogates surface localization: mutant protein is retained in the endoplasmic reticulum/Golgi apparatus, which is predicted to result from deleterious conformational and biochemical changes. ICOSL^N219K diminished B cell costimulation of T cells, providing a compelling basis for the observed defect in antibody and memory B cell generation. Interestingly, ICOSL^N219K also impaired migration of lymphocytes and neutrophils across endothelial cells, which normally express ICOSL. These defects likely contributed to the altered adaptive immunity and neutropenia observed in the patient, respectively. Our study identifies human ICOSLG deficiency as a novel cause of a combined immunodeficiency.

A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer

Therapies targeting epidermal growth factor receptor (EGFR) have variable and unpredictable responses in breast cancer. Screening triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), we identify a subset responsive to EGFR inhibition by gefitinib, which displays heterogeneous expression of wild-type EGFR. Deep single-cell RNA sequencing of 3,500 cells from an exceptional responder identified subpopulations displaying distinct biological features, where elevated EGFR expression was significantly enriched in a mesenchymal/stem-like cellular cluster. Sorted EGFR^hi subpopulations exhibited enhanced stem-like features, including ALDH activity, sphere-forming efficiency, and tumorigenic and metastatic potential. EGFR^hi cells gave rise to EGFR^hi and EGFR^lo cells in primary and metastatic tumors, demonstrating an EGFR-dependent expansion and hierarchical state transition. Similar tumorigenic EGFR^hi subpopulations were identified in independent PDXs, where heterogeneous EGFR expression correlated with gefitinib sensitivity. This provides new understanding for an EGFR-dependent hierarchy in TNBC and for patient stratification for therapeutic intervention.

A biochemical framework for eIF4E-dependent mRNA export and nuclear recycling of the export machinery

The eukaryotic translation initiation factor eIF4E acts in the nuclear export and translation of a subset of mRNAs. Both of these functions contribute to its oncogenic potential. While the biochemical mechanisms that underlie translation are relatively well understood, the molecular basis for eIF4E's role in mRNA export remains largely unexplored. To date, over 3000 transcripts, many encoding oncoproteins, were identified as potential nuclear eIF4E export targets. These target RNAs typically contain a ∼50-nucleotide eIF4E sensitivity element (4ESE) in the 3' UTR and a 7-methylguanosine cap on the 5' end. While eIF4E associates with the cap, an unknown factor recognizes the 4ESE element. We previously identified cofactors that functionally interacted with eIF4E in mammalian cell nuclei including the leucine-rich pentatricopeptide repeat protein LRPPRC and the export receptor CRM1/XPO1. LRPPRC simultaneously interacts with both eIF4E bound to the 5' mRNA cap and the 4ESE element in the 3' UTR. In this way, LRPPRC serves as a specificity factor to recruit 4ESE-containing RNAs within the nucleus. Further, we show that CRM1 directly binds LRPPRC likely acting as the export receptor for the LRPPRC-eIF4E-4ESE RNA complex. We also found that Importin 8, the nuclear importer for cap-free eIF4E, imports RNA-free LRPPRC, potentially providing both coordinated nuclear recycling of the export machinery and an important surveillance mechanism to prevent futile export cycles. Our studies provide the first biochemical framework for the eIF4E-dependent mRNA export pathway.

Transcriptome Analysis of Human Reninomas as an Approach to Understanding Juxtaglomerular Cell Biology

Renin, a key component in the regulation of blood pressure in mammals, is produced by the rare and highly specialized juxtaglomerular cells of the kidney. Chronic stimulation of renin release results in a recruitment of new juxtaglomerular cells by the apparent conversion of adjacent smooth muscle cells along the afferent arterioles. Because juxtaglomerular cells rapidly dedifferentiate when removed from the kidney, their developmental origin and the mechanism that explains their phenotypic plasticity remain unclear. To overcome this limitation, we have performed RNA expression analysis on 4 human renin-producing tumors. The most highly expressed genes that were common between the reninomas were subsequently used for in situ hybridization in kidneys of 5-day-old mice, adult mice, and adult mice treated with captopril. From the top 100 genes, 10 encoding for ligands were selected for further analysis. Medium of human embryonic kidney 293 cells transfected with the mouse cDNA encoding these ligands was applied to (pro)renin-synthesizing As4.1 cells. Among the ligands, only platelet-derived growth factor B reduced the medium and cellular (pro)renin levels, as well as As4.1 renin gene expression. In addition, platelet-derived growth factor B-exposed As4.1 cells displayed a more elongated and aligned shape with no alteration in viability. This was accompanied by a downregulated expression of α-smooth muscle actin and an upregulated expression of interleukin-6, suggesting a phenotypic shift from myoendocrine to inflammatory. Our results add 36 new genes to the list that characterize renin-producing cells and reveal a novel role for platelet-derived growth factor B as a regulator of renin-synthesizing cells.

Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms

BACKGROUND

Genome-wide expression profiling is increasingly being used to identify transcriptional changes induced by drugs and environmental stressors. In this context, the Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system (TG-GATEs) project generated transcriptional profiles from rat liver samples and human/rat cultured primary hepatocytes exposed to more than 100 different chemicals.

OBJECTIVES

To assess the capacity of the cell culture models to recapitulate pathways induced by chemicals in vivo, we leveraged the TG-GATEs data set to compare the early transcriptional responses observed in the liver of rats treated with a large set of chemicals with those of cultured rat and human primary hepatocytes challenged with the same compounds in vitro.

METHODS

We developed a new pathway-based computational pipeline that efficiently combines gene set enrichment analysis (GSEA) using pathways from the Reactome database with biclustering to identify common modules of pathways that are modulated by several chemicals in vivo and in vitro across species.

RESULTS

We found that some chemicals induced conserved patterns of early transcriptional responses in in vitro and in vivo settings, and across human and rat genomes. These responses involved pathways of cell survival, inflammation, xenobiotic metabolism, oxidative stress, and apoptosis. Moreover, our results support the transforming growth factor beta receptor (TGF-βR) signaling pathway as a candidate biomarker associated with exposure to environmental toxicants in primary human hepatocytes.

CONCLUSIONS

Our integrative analysis of toxicogenomics data provides a comprehensive overview of biochemical perturbations affected by a large panel of chemicals. Furthermore, we show that the early toxicological response occurring in animals is recapitulated in human and rat primary hepatocyte cultures at the molecular level, indicating that these models reproduce key pathways in response to chemical stress. These findings expand our understanding and interpretation of toxicogenomics data from human hepatocytes exposed to environmental toxicants.

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

Background

Microarrays have revolutionized breast cancer (BC) research by enabling studies of gene expression on a transcriptome-wide scale. Recently, RNA-Sequencing (RNA-Seq) has emerged as an alternative for precise readouts of the transcriptome. To date, no study has compared the ability of the two technologies to quantify clinically relevant individual genes and microarray-derived gene expression signatures (GES) in a set of BC samples encompassing the known molecular BC’s subtypes. To accomplish this, the RNA from 57 BCs representing the four main molecular subtypes (triple negative, HER2 positive, luminal A, luminal B), was profiled with Affymetrix HG-U133 Plus 2.0 chips and sequenced using the Illumina HiSeq 2000 platform. The correlations of three clinically relevant BC genes, six molecular subtype classifiers, and a selection of 21 GES were evaluated.

Results

16,097 genes common to the two platforms were retained for downstream analysis. Gene-wise comparison of microarray and RNA-Seq data revealed that 52% had a Spearman’s correlation coefficient greater than 0.7 with highly correlated genes displaying significantly higher expression levels. We found excellent correlation between microarray and RNA-Seq for the estrogen receptor (ER; r_s = 0.973; 95% CI: 0.971-0.975), progesterone receptor (PgR; r_s = 0.95; 0.947-0.954), and human epidermal growth factor receptor 2 (HER2; r_s = 0.918; 0.912-0.923), while a few discordances between ER and PgR quantified by immunohistochemistry and RNA-Seq/microarray were observed. All the subtype classifiers evaluated agreed well (Cohen’s kappa coefficients >0.8) and all the proliferation-based GES showed excellent Spearman correlations between microarray and RNA-Seq (all r_s >0.965). Immune-, stroma- and pathway-based GES showed a lower correlation relative to prognostic signatures (all r_s >0.6).

Conclusions

To our knowledge, this is the first study to report a systematic comparison of RNA-Seq to microarray for the evaluation of single genes and GES clinically relevant to BC. According to our results, the vast majority of single gene biomarkers and well-established GES can be reliably evaluated using the RNA-Seq technology.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1008) contains supplementary material, which is available to authorized users.